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BioC 3.4: CHECK report for nethet on morelia

This page was generated on 2017-04-15 16:26:07 -0400 (Sat, 15 Apr 2017).

Package 836/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
nethet 1.6.0
Nicolas Staedler
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/nethet
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: nethet
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings nethet_1.6.0.tar.gz
StartedAt: 2017-04-15 05:38:17 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 05:41:29 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 191.3 seconds
RetCode: 0
Status:  OK 
CheckDir: nethet.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings nethet_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/nethet.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nethet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nethet’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘nethet’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
MStepGlasso: no visible global function definition for ‘cov.wt’
agg.pval: no visible global function definition for ‘quantile’
aggpval: no visible global function definition for ‘optimize’
aggpval : <anonymous>: no visible global function definition for
  ‘quantile’
aic.glasso: no visible global function definition for ‘var’
bic.glasso: no visible global function definition for ‘var’
cv.glasso: no visible global function definition for ‘var’
cv.glasso: no visible binding for global variable ‘var’
diffnet_multisplit: no visible global function definition for
  ‘optimize’
diffnet_multisplit: no visible binding for global variable ‘median’
diffnet_multisplit: no visible global function definition for ‘median’
diffregr_multisplit: no visible global function definition for
  ‘optimize’
diffregr_multisplit: no visible global function definition for ‘median’
diffregr_singlesplit: no visible global function definition for ‘coef’
diffregr_singlesplit: no visible global function definition for ‘lm’
error.bars: no visible global function definition for ‘segments’
est2.my.ev2.diffregr: no visible global function definition for ‘var’
est2.my.ev3.diffregr: no visible global function definition for ‘var’
est2.ww.mat.diffregr: no visible global function definition for ‘var’
est2.ww.mat2.diffregr: no visible global function definition for ‘var’
export_network: no visible global function definition for ‘write.csv’
func.uinit: no visible global function definition for ‘kmeans’
getinvcov: no visible global function definition for ‘rbeta’
ggmgsa_multisplit: no visible binding for global variable ‘median’
gsea.iriz.scale: no visible global function definition for ‘pnorm’
gsea.iriz.shift: no visible global function definition for ‘pnorm’
lambda.max: no visible global function definition for ‘var’
logratio.diffregr: no visible global function definition for ‘dnorm’
mcov: no visible global function definition for ‘cov.wt’
mcov: no visible global function definition for ‘var’
mixglasso_init: no visible global function definition for ‘cov.wt’
my.p.adjust: no visible global function definition for ‘p.adjust’
my.ttest: no visible global function definition for ‘var’
my.ttest2: no visible global function definition for ‘var’
perm.diffregr_teststat: no visible global function definition for
  ‘coef’
perm.diffregr_teststat: no visible global function definition for ‘lm’
plot.diffnet: no visible global function definition for ‘hist’
plot.diffnet: no visible global function definition for ‘abline’
plot.diffnet: no visible global function definition for ‘legend’
plot.diffregr: no visible global function definition for ‘hist’
plot.diffregr: no visible global function definition for ‘abline’
plot.diffregr: no visible global function definition for ‘legend’
plot.ggmgsa: no visible global function definition for ‘boxplot’
plot.nethetclustering: no visible global function definition for ‘pdf’
plot.nethetclustering: no visible global function definition for ‘grey’
plot.nethetclustering: no visible global function definition for
  ‘legend’
plot.nethetclustering: no visible global function definition for
  ‘dev.off’
plot_2networks: no visible global function definition for ‘par’
scatter_plot : <anonymous>: no visible global function definition for
  ‘cor’
screen_cv.glasso: no visible global function definition for ‘var’
screen_cv.glasso: no visible binding for global variable ‘var’
screen_cv1se.lasso: no visible global function definition for ‘coef’
screen_cvfix.lasso: no visible global function definition for ‘coef’
screen_cvmin.lasso: no visible global function definition for ‘coef’
screen_cvsqrt.lasso: no visible global function definition for ‘coef’
screen_cvtrunc.lasso: no visible global function definition for ‘coef’
screen_mb: no visible global function definition for ‘var’
screen_mb: no visible binding for global variable ‘var’
screen_mb2 : <anonymous>: no visible global function definition for
  ‘lines’
screen_mb2 : <anonymous>: no visible global function definition for
  ‘coef’
shapiro_screen : <anonymous>: no visible global function definition for
  ‘shapiro.test’
shapiro_screen: no visible global function definition for ‘p.adjust’
sim_mix_networks : <anonymous>: no visible global function definition
  for ‘rnorm’
t2cov.lr: no visible global function definition for ‘var’
t2cov.lr: no visible global function definition for ‘pchisq’
t2diagcov.lr: no visible global function definition for ‘var’
t2diagcov.lr: no visible global function definition for ‘pchisq’
test.sd: no visible global function definition for ‘var’
test.sd: no visible global function definition for ‘pnorm’
twosample_single_regr: no visible global function definition for ‘coef’
twosample_single_regr: no visible global function definition for ‘lm’
Undefined global functions or variables:
  abline boxplot coef cor cov.wt dev.off dnorm grey hist kmeans legend
  lines lm median optimize p.adjust par pchisq pdf pnorm quantile rbeta
  rnorm segments shapiro.test var write.csv
Consider adding
  importFrom("grDevices", "dev.off", "grey", "pdf")
  importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines",
             "par", "segments")
  importFrom("stats", "coef", "cor", "cov.wt", "dnorm", "kmeans", "lm",
             "median", "optimize", "p.adjust", "pchisq", "pnorm",
             "quantile", "rbeta", "rnorm", "shapiro.test", "var")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
het_cv_glasso       27.269  0.108  27.405
mixglasso           18.172  0.181  18.635
ggmgsa_multisplit   14.979  0.043  15.036
diffregr_multisplit 10.873  0.076  10.958
diffnet_multisplit   5.072  0.041   5.215
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/nethet.Rcheck/00check.log’
for details.


nethet.Rcheck/00install.out:

* installing *source* package ‘nethet’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c betamat_diffnet.c -o betamat_diffnet.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o nethet.so betamat_diffnet.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.4-bioc/meat/nethet.Rcheck/nethet/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nethet)

nethet.Rcheck/nethet-Ex.timings:

nameusersystemelapsed
aggpval0.0060.0010.007
bwprun_mixglasso3.8360.0693.920
diffnet_multisplit5.0720.0415.215
diffnet_singlesplit2.4330.0082.444
diffregr_multisplit10.873 0.07610.958
diffregr_singlesplit0.6780.0010.680
dot_plot0.9770.0050.984
export_network0.4610.0030.463
generate_2networks0.0620.0010.064
generate_inv_cov0.0890.0720.160
ggmgsa_multisplit14.979 0.04315.036
gsea.iriz0.0080.0000.008
het_cv_glasso27.269 0.10827.405
invcov2parcor0.0020.0000.002
invcov2parcor_array0.0040.0000.004
logratio0.0020.0000.002
mixglasso18.172 0.18118.635
plot_2networks0.3030.0030.359
scatter_plot2.7720.0143.190
screen_aic.glasso0.7680.0010.808
screen_bic.glasso0.6970.0010.700
screen_cv.glasso1.8410.0071.850
screen_cv1se.lasso0.2290.0030.233
screen_cvfix.lasso0.2520.0000.283
screen_cvmin.lasso0.2520.0000.286
screen_cvsqrt.lasso0.2640.0030.312
screen_cvtrunc.lasso0.2580.0010.303
screen_mb0.0120.0000.013
sim_mix0.0050.0020.007
sim_mix_networks0.0090.0000.012